Biology subjects

Kumar, N.

Publications and source records attributed to Kumar, N..

At least 55 records · Page 3Linked to original sources

bioRxiv2025

Neural Mechanisms Underlying Approach and Avoidance Tendencies in Alcohol Use: An Electrophysiological Investigation

Background: A growing body of research highlights the differential role of approach and avoidance tendencies toward alcohol cues in the development and maintenance of harmful drinking behavior. Some individuals involved in alcohol consumption show an automatic approach towards alcohol-related stimuli, whereas others demonstrate avoidance, suggesting the need to understand the neurocognitive mechanisms underlying these automatic tendencies. Methods: The current study employed an Alcohol Approach-Avoidance Task (A-AAT) with electroencephalography (EEG) to investigate neural responses among individuals with alcohol approach and avoidance tendencies. Alcohol group participants were categorized into approach and avoidance subgroups based on their behavioral tendencies following A-AAT administration. Findings: Results revealed significant attenuation in P3 and FN400 amplitudes at frontal and parietal sites, respectively, in the alcohol-approach participants compared to both the alcohol-avoidance and non-alcohol participants. These findings suggest weakened controlled cue processing and impaired stimulus-response conflict resolution in individuals with stronger approach tendencies. Notably, right prefrontal activity exhibited prominent differences between the approach and avoidance groups, highlighting its potential role in regulating automatic alcohol-related responses. Implications: The identified ERP markers provide clinical utility for assessing alcohol approach tendencies and monitoring the progress of intervention. Findings further emphasize the importance of individually tailored targeted interventions aimed at reducing harmful alcohol consumption behavior by altering alcohol approach tendencies.

neuroscience↗

bioRxiv2025

PEPlife2: A Updated Repository of the Half-life of Peptides

This manuscript presents an updated version of PEPlife, a manually curated database that provides comprehensive information on peptide half-life. The updated version, PEPlife2, includes 4,412 entries, compared to 2,229 entries in the previous version. Each entry contains detailed information that include experimental methods used to determine half-life, chemical modifications, biological activity, routes of administration, and other relevant data. The database encompasses 402 proteins and 1,781 peptides, derived from 105 unique assays. In addition to natural peptide sequences, PEPlife2 includes cyclic peptides and chemically modified peptides, such as those with N- and C-terminal modifications. To provide structural insights, peptide and protein structures are sourced from the Protein Data Bank (PDB) or predicted using PEPstrMOD. To support the scientific community, we have developed a user-friendly interface and integrated advanced analytical tools, including BLAST, Smith-Waterman, GGSEARCH, CLUSTALW, and MUSTANG. The updated database is accessible at: https://webs.iiitd.edu.in/raghava/peplife2/. Authors BiographyO_LIUrooj Alam is currently pursuing a Masters degree in Computational Biology at the Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India. C_LIO_LIKunal Chaudhary is working as Ph.D. in Computational biology from Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India C_LIO_LINishant Kumar is currently working as Ph.D. in Computational biology from Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India C_LIO_LIRitu Tomer is currently working as Ph.D. in Computational biology from Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India C_LIO_LISumeet Patiyal is currently working as a postdoctoral visiting fellow Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA. C_LIO_LIGajendra P. S. Raghava is currently working as Professor and Head of Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India. C_LI

bioinformatics↗

bioRxiv2025

An efficient protocol to derive primordial germ cell like cells in vitro from murine embryonic stem cells.

Primordial germ cells (PGCs) are the precursors of germ cells, specified from a subset of epiblast stem cells at the post-implantation stage of mammalian embryonic development. Over the past decade, primordial germ cell-like cells (PGCLCs) have been successfully derived in vitro from mouse and human embryonic stem cells (ESCs). These PGCLCs can further differentiate into mature sperm upon transplantation into neonatal testes. Such advancements offer promising strategies to address male infertility, which affects approximately 15% of couples worldwide. The discovery of induced pluripotent stem cells (iPSCs), which possess similar potential to ESCs, further raises hope for patient-specific therapeutic interventions. However, a major challenge remains: the low efficiency of in vitro PGCLC differentiation. To overcome this, we developed an optimized PGCLC differentiation strategy using a Dppa3-mCherry knock-in reporter mouse ESC line, TDM11. By testing various culture conditions, we identified ascorbic acid as a potent inducer of PGCLC differentiation from ESCs, providing a potential avenue for enhancing in vitro germ cell derivation.

developmental biology↗

bioRxiv2025

Interaction between Model-based and Model-free Mechanisms in Motor Learning

Motor learning can be driven by distinct mechanisms--habitual, model-free processes, and strategic, model-based processes--depending on the magnitude and context of movement errors. Although small and large errors are known to engage distinct motor learning mechanisms--model-free (implicit) or model-based (explicit), respectively--it remains unclear whether successfully deploying one mechanism might hamper the engagement of the other in subsequent learning tasks. Here, we investigated how prior engagement of a particular mechanism biases future adaptations, even when the new task context typically favours the alternative strategy. Across three experiments (N=82), participants performed reaching movements to targets that either remained fixed or "jumped" mid-movement by small (15{degrees}) or large (30{degrees}, 45{degrees}, or 60{degrees}) angles. When first exposed to small errors (15{degrees}), participants exhibited persistent aftereffects in subsequent catch trials and stable reaction times (RTs), hallmarks of a model-free, habitual process. Surprisingly, even when switching to larger error magnitudes later, these participants continued to show robust aftereffects and did not elevate RTs-- indicating a carryover of model-free learning. Conversely, participants who initially experienced large errors showed minimal aftereffects and flexible RT modulation consistent with model-based strategies; this bias persisted in later sessions with smaller errors, leading to reduced habitual aftereffects. Notably, inserting a washout phase to reset baseline performance did not abolish these mechanistic biases, highlighting that the initial engagement of either model-free or model-based processes leaves a durable imprint on subsequent adaptations. Taken together, these findings demonstrate that motor learning is shaped not only by ongoing task demands (e.g., error magnitude) but also by an individuals prior learning history. Understanding how initial learning experiences constrain future adaptations has broad implications for designing interventions and training protocols in motor rehabilitation and skill acquisition. Statement of SignificanceMotor learning involves distinct mechanisms: habitual, model-free processes (driven by gradual stimulus-response associations) and strategic, model-based processes (guided by explicit adjustments). This study demonstrates that initial engagement of one mechanism biases subsequent adaptations, even when task demands shift to favor the alternative. The findings suggest that motor learning is a hierarchical process shaped by cumulative contextual experiences. Our results have highlighted how early learning establishes neural or cognitive frameworks that constrain future adaptations, prioritizing efficiency over flexibility. This has implications for designing motor training or rehabilitation protocols: initiating learning with model-based strategies (via large errors) may preserve adaptability, while model-free training (via small errors) risks anchoring rigid habits. By elucidating how prior mechanisms bias ongoing learning, this work advances our understanding of motor memory interactions and their real-world applications in skill acquisition and recovery.

neuroscience↗

bioRxiv2025

mRNA-delivered neutralizing antibodies confer protection against SARS-CoV-2 variant in the lower and upper respiratory tract

Monoclonal antibodies (mAbs) have been developed as effective biological countermeasures against a range of human diseases. The high cost of antibody production and manufacturing limits its clinical application and widespread use. The mRNA-lipid nanoparticle (mRNA-LNP) is a versatile platform for development of vaccines and protein-replacement therapeutics. Since the COVID-19 pandemic, a number of neutralizing mAbs against SARS-CoV-2 have been identified with several being used clinically under emergency authorization. Herein, we report the design and generation of mRNA-LNPs expressing two SARS-CoV-2 neutralizing mAbs, 76E1 and LY1404, which respectively target the viral spike proteins fusion peptide (FP) epitope within the S2 subunit and the receptor-binding domain (RBD) within the S1 subunit. We show a single intramuscular administration of mRNA-LNPs results in efficient LY1404 and 76E1 mAb production in mice which is sustained for 7-14 days. Further, we evaluate the protective efficacy of mRNA-LNP formulations encoding the two antibodies in mouse and hamster models challenged with different SARS-CoV-2 viral strains. The data demonstrate that a single administration of mRNA-LNP encoding the more broadly neutralizing antibody 76E1 confers significant protection against the immune-evasive SARS-CoV-2 Omicron variant BQ.1 in both the upper and lower respiratory tract of the hamsters, indicating its potential impact on limiting both viral disease and viral acquisition. Together, our study expands the potential of the mRNA-LNP platform to deliver therapeutic antibodies for rapid prevention or treatment of pathogenic infections.

microbiology↗

bioRxiv2025

Single-cell atlas of patient-derived cervical organoids uncovers epithelial immune heterogeneity and intercellular crosstalk during Chlamydia infection

The uterine cervix is a critical mucosal interface that balances immune defense and reproductive function, yet how its distinct epithelial compartments coordinate responses to infection remains unclear. Here, we integrate patient-derived 3D cervical organoids, single-cell transcriptomics and native tissue analysis to construct a high-resolution atlas of epithelial cell diversity and immune dynamics during Chlamydia trachomatis infection. We demonstrate that cervical organoids precisely mirror native tissue at both transcriptional and cellular levels, identifying epithelial subtypes with region-specific immune specializations. Upon infection, ectocervical epithelia reinforce barrier integrity, whereas endocervical epithelia, particularly uninfected bystander cells, exhibit extensive transcriptional reprogramming characterized by robust interferon activation, antigen presentation, and antimicrobial defense. Infection profoundly reshapes epithelial intercellular communication, positioning bystander cells as central signaling hubs that coordinate immune responses and tissue regeneration. Our findings highlight a sophisticated epithelial-intrinsic immune network critical for cervical mucosal defense and establish a physiologically relevant platform for studying human host-pathogen interactions and guiding targeted mucosal therapies against reproductive tract infections and pathologies.

systems biology↗

bioRxiv2025

TGF-β inhibitor SB431542 suppresses coronavirus replication through multistep inhibition

The COVID-19 pandemic highlighted the critical need for broad-spectrum antivirals with high resistance barriers. Here, we demonstrate that SB431542, a selective TGF-{beta} receptor I (ALK5) inhibitor, exhibits potent antiviral activity against SARS-CoV-2 through unprecedented multitargeted mechanisms. Through comprehensive in vitro, and in silico analyses, we identified that SB431542 directly binds to SARS-CoV-2 ORF3a and disrupt its canonical function in inhibiting autophagosome-lysosome fusion. This interaction restored lysosomal acidification and normalized perinuclear LAMP-1 localization, significantly impairing virion assembly as evidenced by disrupted nucleocapsid-RNA association and reduced intracellular viral titers. Additionally, SB431542 downregulated the CLEAR network genes responsible for lysosomal biogenesis, further restricting viral egress pathways. Our temporal analyses revealed that at later infection stages (36-48 hpi), SARS-CoV-2 exploits TGF-{beta}-induced lysosomal membrane permeabilization (LMP) and apoptosis for viral release--processes effectively inhibited by SB431542 through suppression of GADD45b and BAX expression. These multiple mechanisms resulted in an exceptional EC50 of 515 nM against SARS-CoV-2. In vivo efficacy was demonstrated in embryonated chicken eggs, where SB431542 conferred dose-dependent protection against lethal infectious bronchitis virus (IBV) challenge, with a favourable therapeutic index of 34.54. Remarkably, sequential passaging of SARS-CoV-2 for 50 generations under SB431542 selection pressure failed to generate resistant variants, contrasting sharply with the rapid resistance emergence typical of direct-acting antivirals. These findings establish SB431542 as a promising broad-spectrum coronavirus inhibitor with a unique triple-mechanism approach that simultaneously targets viral entry via TGF-{beta}/Smad modulation, disrupts ORF3a-mediated lysosomal dysfunction affecting assembly, and attenuates TGF-{beta}-induced apoptosis during late-stage infection-- collectively imposing multiple selective constraints that impede escape mutation development. ImportanceThe COVID-19 pandemic highlighted the urgent need for antiviral drugs with high barriers to resistance. This study reveals that SB431542, a drug previously developed to inhibit TGF-{beta} signaling, exhibits remarkable effectiveness against SARS-CoV-2 through an unprecedented triple-mechanism approach. Unlike conventional antivirals that target a single viral component, SB431542 simultaneously disrupts viral entry, assembly, and release by binding to the viral ORF3a protein and modulating host cellular processes. Most importantly, SARS-CoV-2 failed to develop resistance against SB431542 even after 50 generations of exposure--a significant advantage over current therapeutics that quickly lose effectiveness due to viral mutations. Our findings also uncover that coronaviruses exploit both lysosomal dysfunction and programmed cell death to spread efficiently, providing new targets for therapeutic intervention. This research establishes SB431542 as a promising broad-spectrum coronavirus inhibitor and demonstrates the value of targeting host-virus interactions to overcome antiviral resistance.

microbiology↗

bioRxiv2025

DZNep-induced single point mutation (M236I) in poxviral 2'-O-methyltransferase enhances mRNA stability and translation efficiency

Poxviruses encode two highly conserved S-adenosylmethionine (SAM)-dependent methyltransferases for mRNA capping. While D1L facilitates translation via cap-0 formation, the role of VP39-mediated cap-1 modification has been canonically restricted to shield viral mRNA from cytoplasmic pattern-recognition receptors (PRRs). Here, we uncover a novel function of VP39 by demonstrating that prolonged exposure to the SAM cycle inhibitor DZNep selected a virus escape mutant harbouring a point mutation (M236I) in VP39. VP39_mut bypasses S-adenosylhomocysteine (SAH)-mediated feedback inhibition, enhancing 2-O-methylation of viral transcripts and promoting their association with active translation machinery. Consequently, VP39_mut significantly improves viral protein translation, replicative fitness, and yields across species. Notably, VP39_mut-capped in vitro transcribed (IVT) mRNA exhibited [~]2.7-fold higher protein expression compared to VP39_wt, the standard tool for IVT applications. These findings reveal a unique resistance mechanism and provide critical insights into poxvirus mRNA biology while underscoring the potential of optimized VP39 for advancing mRNA-based therapeutics and vaccine production.

microbiology↗

bioRxiv2025

Highly Pathogenic Avian Influenza A (H5N1) Clade 2.3.2.1a virus infection in domestic cats, India, 2025

In January 2025, the highly pathogenic avian influenza A(H5N1) virus clade 2.3.2.1a infection was detected in domestic cats and whole-genome sequencing of two cat H5N1 isolates was performed using the Oxford Nanopore MinION sequencing platform. Phylogenetic analysis revealed the circulation of triple reassortant viruses in cats. Although cat viruses lacked classic mammalian adaptation markers they carried mutations associated with enhanced polymerase activity in mammalian cells and increased affinity for 2-6 sialic acid receptor suggesting their potential role in facilitating infection in cats. The identification of reassortant HPAI H5N1 clade 2.3.2.1a viruses in domestic cats in India highlights the urgent need for enhanced surveillance in domestic poultry, wild birds, and mammals, including humans, to track genomic diversity and molecular evolution of circulating strains.

microbiology↗

bioRxiv2025

Addressing efficacy of everyday hygiene cleansing products in context of sustainable handwashing behavior in the post-pandemic era

Simple hygiene behaviour such as washing hands is key to improving health of individuals and reducing community transmission of communicable diseases such as respiratory and enteric infections. Consistent and relentless messaging by global and local health authorities had resulted in heightened hygiene awareness amongst the public during the COVID-19 pandemic. Unfortunately, many of the hygiene behaviours practiced during the pandemic have proven to be unsustainable in the immediate period following the pandemic. While CDC guidelines suggest washing hands with soap for a minimum of 20 seconds to prevent the spread of germs, a hygiene interventions effectiveness must be evaluated in context of the prevalent hygiene behaviour. Here we report our findings from an observational study conducted across India, Pakistan, Saudi Arabia, and United Arab Emirates focusing on handwashing habit of individuals in the post-pandemic period. Across all geographies, the time spent for lathering product on skin (contact time) for a significant majority of individuals recruited for the study was found to be 10 seconds and less. To ensure that marketed hygiene formulations such as liquid cleansers and sanitizers are efficacious in inactivating pathogens under conditions practiced by the majority as a part of their daily hand washing practices, we have investigated the in-vitro antimicrobial efficacy of several hygiene cleansing formulations at 10 seconds of contact time. Our results show that well-formulated cleansing solutions can reduce the input titre of both bacterial and viral pathogens by 99.9% or more, even with brief contact. With the global resurgence of both existing and emerging pathogens in the post-pandemic world, promoting sustainable handwashing practices for infection prevention remains a challenge as it is deeply rooted in the socio-economic fabric of many countries. Therefore, it is crucial to conduct regular studies like this to reassure end-users and combat complacency regarding the composition of everyday hygiene products. HighlightsO_LIStudies of handwashing behavior in 4 countries reveals significantly short lathering duration C_LIO_LIAntimicrobial efficacy testing of marketed products was conducted against a range of pathogens C_LIO_LISuitably formulated hygiene products can inactivate pathogens at short durations of contact C_LI

microbiology↗

bioRxiv2025

Local traveling waves of cytosolic calcium elicited by defense signals or wounding are propagated by distinct mechanisms

Cytosolic Ca2+ signatures with specific spatiotemporal patterns play crucial roles in plant responses to biotic and abiotic stresses. Perception of microbe- or damage-associated molecular patterns (MAMPs or DAMPs) initiates signaling cascades that represent the first layer of plant defense against pathogens known as pattern-triggered immunity (PTI). During PTI, MAMP/DAMP-induced cytosolic Ca2+ fluxes serve as essential messengers in the initiation and transmission of defense signals at the cellular, whole organ, and systemic levels. However, the specific patterns of these Ca2+ signatures in response to different pathogen cues, and the mechanisms that encode them, remain largely unexplored. In this study, we quantitatively assessed Ca2+ signatures at the single-cell level as well as the local traveling Ca2+ waves induced by global treatment of Arabidopsis cotyledons with MAMPs or DAMPs. We demonstrated that MAMPs induced distinct local spatiotemporal Ca2+ responses in epidermal pavement cells, with Ca2+ traveling waves consistently initiated from a subset of cells and spreading in an approximately radial pattern. These local traveling waves propagated at a slow but constant speed of approximately 1 {micro}m/s and spread to a limited number of neighboring cells. In contrast, wound-induced traveling waves displayed a diffusion-like decay pattern that moved rapidly away from the wounded cell but with diminishing speed over time and distance. Mathematical modeling supported a calcium-induced calcium release mechanism that could recapitulate the constant wave speed induced by MAMPs. These findings contribute to a deeper understanding of plant defense-related Ca2+ signaling mechanisms as well as how defense responses are spatially restricted within tissues. One Sentence SummaryA slow, local traveling wave of calcium is initiated from a subset of epidermal cells during plant immune signaling.

cell biology↗

bioRxiv2025

The Single-Cell Landscape of Peripheral and Tumor-infiltrating Immune Cells in HPV- HNSCC

Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer worldwide. HPV-negative HNSCC, which arises in the upper airway mucosa, is particularly aggressive, with nearly half of patients succumbing to the disease within five years and limited response to immune checkpoint inhibitors compared to other cancers. There is a need to further explore the complex immune landscape in HPV-negative HNSCC to identify potential therapeutic targets. Here, we integrated two single-cell RNA sequencing datasets from 29 samples and nearly 300,000 immune cells to investigate immune cell dynamics across tumor progression and lymph node metastasis. Notable shifts toward adaptative immune cell populations were observed in the 14 distinct HNSCC-associated peripheral blood mononuclear (PBMCs) and 21 tumor-infiltrating immune cells (TICs) considering disease stages. All PBMCs and TICs revealed unique molecular signatures correlating with lymph node involvement; however, broadly, TICs increased ligand expression among effector cytokines, growth factors, and interferon-related genes. Pathway analysis comparing PBMCs and TICs further confirmed active cell signaling among Monocyte-Macrophage, Dendritic cell, Natural Killer (NK), and T cell populations. Receptor-ligand analysis revealed significant communication patterns shifts among TICs, between CD8+ T cells and NK cells, showing heightened immunosuppressive signaling that correlated with disease progression. In locally invasive HPV-negative HNSCC samples, highly multiplexed immunofluorescence assays highlighted peri-tumoral clustering of exhausted CD8+ T and NK cells, alongside their exclusion from intra-tumoral niches. These findings emphasize cytotoxic immune cells as valuable biomarkers and therapeutic targets, shedding light on the mechanisms by which the HNSCC sustainably evades immune responses.

cancer biology↗

bioRxiv2025

Distinct region-specific neutralization profiles of contemporary HIV-1 clade C against best-in-class broadly neutralizing antibodies

Broadly neutralizing antibodies (bnAb) have been clinically proven to be an excellent choice for HIV-1 prevention. However, the relative effectiveness of best-in-class bnAbs against regionally relevant circulating HIV-1 forms is not clear. In the present study, we compared the degree of neutralization sensitivity of contemporary HIV-1 Indian clade C with that of South African origin. Phylogenetic analysis revealed that these clade C viruses continue to evolve distinctly from one another. Env-pseudotyped viruses prepared using contemporary HIV-1 clade C env genes (N=115) obtained from nine geographically distinct sites in India (between 2020-2023) were found to be most sensitive to V3-directed bnAbs 10-1074 and BG18, and second generation CD4 binding site (CD4bs) directed bnAbs (VRC07, N6 and 1-18), however they were found to be significantly resistant to V1/V2 apex directed bnAbs. Moreover, we observed that the degree of sensitivity varied between contemporary Indian and South African clade C viruses. Differences in degree of neutralization susceptibility were associated with differences observed in key residues that form bnAb contact sites, gp120 loop lengths and the number of N-linked glycans in the V4 hypervariable region. Interestingly, the second generation CD4bs bnAbs (VRC07, N6, 1-18) showed neutralization of VRC01 and 3BNC117 resistant viruses but with 2-7-fold reduced potency compared to the VRC01 sensitive counterparts, likely due to the enrichment of resistance associated residues observed in loop D. Predictive analysis indicated that combination of BG18, N6 and PGDM1400 can provide over 95% neutralization coverage at 1g/mL of contemporary India clade C, an observation found to be distinct to that reported for the Africa clade C viruses. Taken together, we found distinct neutralization patterns and env signatures associated with resistance to key bnAbs. Our study highlights that towards achieving clinical effectiveness, both the complementarity of bnAb classes and the regionally relevant HIV forms need to be considered. Author summaryWhile the development of vaccines to prevent HIV infection remains a global priority, their potential effectiveness is limited by the extraordinarily diversified circulating forms of HIV-1. The prospect of best-in-class bnAbs as potential prevention option has been demonstrated in several studies including the Phase II Antibody Mediated Prevention (AMP) trial; however, to be broadly applicable, bnAbs will need to overcome the substantial variability of HIV env. The present study highlights that the contemporary HIV-1 clade C viruses are evolving to be less sensitive to the best-in-class bnAbs and HIV-1 clade C that predominates in India and South Africa vary in their degree of susceptibility to best-in-class clinically relevant bnAbs. This indicates differences in the antigenic properties between globally circulating HIV-1 clade C at a population level. Overall, the outcome of this study highlights the need for periodic assessment of sequence and neutralization profiles of the circulating regionally relevant HIV-1 forms towards prioritizing the bnAb combination suitable for effective intervention.

immunology↗

bioRxiv2024

HAIRpred: Prediction of human antibody interacting residues in an antigen from its primary structure

1.In the past, several methods have been developed for predicting conformational B-cell epitopes in antigens that are not specific to any host. Our primary analysis of antibody-antigen complexes indicated a need to develop host-specific B-cell epitopes. In this study, we present a novel approach to predict conformational B-cell epitopes specific to human hosts by focusing on human antibody-interacting residues in antigens. We trained, test and evaluate our models on 277 complexes of human antibody-antigen complexes. Initially, we employed machine learning models based on the binary sequence profile of antigens, achieving a maximum area under the receiver operating characteristic curve (AUC) of 0.61. Performance of model improved significantly AUC from 0.61 to 0.67, when evolutionary profiles are used instead of binary profiles. Models developed using embeddings from fine-tuned large language models reached an AUC of 0.61. Additionally, models utilizing predicted surface relative solvent accessibility achieved an AUC of 0.67. Our ensemble model, which combined relative surface accessibility with evolutionary profiles, achieved highest precision with an AUCROC of 0.72. All models in this study were trained using five-fold cross-validation on a training dataset and evaluated on an independent dataset not used for training or testing. Our method outperforms existing approaches on the independent dataset. Furthermore, we used SHAP eXplainable AI (XAI) method to interpret the importance of individual features contributing to the predictions made by our models. To support the scientific community, we have developed a standalone software, and web server, HAIRpred, for predicting human antibody-interacting residues in proteins. https://webs.iiitd.edu.in/raghava/hairpred/. Authors BiographyO_LIRuchir Sahni is currently studying as an integrated BS-MS student at Indian Institute of Science Education and Research (IISER) Pune, India. He is currently working as an Intern on Project position at Department of Computational Biology, Indraprastha Institute of Information Technology (IIIT), New Delhi, India. C_LIO_LINishant Kumar is currently working as Ph.D. in Computational biology from Department of Computational Biology, Indraprastha Institute of Information Technology (IIIT), New Delhi, India. C_LIO_LIGajendra P. S. Raghava is currently working as Professor and Head of Department of Computational Biology, Indraprastha Institute of Information Technology (IIIT), New Delhi, India. C_LI

bioinformatics↗

bioRxiv2024

Soil microbes prefer organic acids over sugars in simulated root exudation

Sugars and organic acids, primary components in plant root exudates, are thought to enhance microbial decomposition of organic matter in the rhizosphere. However, their specific impacts on microbial activity and nutrient mobilisation remain poorly understood. Here, we simulated passive root exudation to investigate the distinct effects of sugars and organic acids on microbial metabolism in the rhizosphere. We released 13C- labelled sugars and/or organic acids via reverse microdialysis into intact meadow and forest soils over 6-hours. We measured substrate-induced microbial respiration, soil organic matter mineralization, metabolite concentrations, and substrate incorporation into lipid-derived fatty acids. Our results reveal a pronounced microbial preference for organic acids over sugars, with organic acids being removed faster from the exudation spot and preferentially respired by microbes. Unlike sugars, organic acids increased concentrations of microbial metabolic byproducts and cations (K, Ca, Mg) near the exudation spot. Our results challenge the prevailing assumption that sugars are the most readily available and rapidly consumed substrates for soil microbes. Microbial preference for organic acids indicates a trade-off between rapid biomass growth and ATP yield. Our findings underscore the significant role of exudate composition in influencing microbial dynamics and nutrient availability, and emphasize the importance of biotic and abiotic feedback mechanisms in the rhizosphere in regulating root exudation.

microbiology↗

bioRxiv2024

The Immunoregulatory Architecture of the Adult Oral Cavity

The immunoregulatory architecture of human oral tissues remains poorly defined despite their central role as barrier interfaces. We present the first integrated single-cell and dual-platform spatial-proteotranscriptomic atlas of oral tissues, profiling >250,000 single-cell transcriptomes and >4 million spatially-resolved cells across 13 niches. Using our AI-enabled AstroSuite (TACIT, Constellation, STARComm, hist2omics), we defined tissue cellular neighborhoods (TCNs) and multicellular interaction modules (MCIMs) in health, revealing peri-epithelial fibroblast-centered hubs enriched for effector cytokines. We harmonized eight fibroblast subtypes (universal, immune, peri-epithelial, peri-vascular, peri-neural, APC-like, stress-responsive, and myofibroblasts) with stress-responsive subtypes partitioning between mucosae (Type I) and glands (Type II). Spatial multiomics mapped receptor-ligand circuits and showed mucosal stress-responsive fibroblasts as immunoregulatory hubs. In chronic periodontitis, niche-aware integration of healthy and diseased datasets revealed rewiring of fibroblast phenotypes and ligand::receptor networks into interdigitated inflammatory and reparative niches. Disease neighborhoods exhibited fragmentation, expansion of MHC-I, MHC-II, and PD-L1 fibroblasts, and predicted spatial engagement with T cells at ectopic lymphoid structures. Drug2Cell analysis highlighted druggable stromal::immune networks. Together, this proteotranscriptomic atlas positions fibroblasts as central architects of structural immunity in human oral tissues and establishes a scalable framework for precision targeting of stromal::immune ecosystems across other barrier organs in health and chronic disease.

cell biology↗

bioRxiv2024

Defining and Controlling Axial Nephron Patterning in Human Kidney Organoids with Synthetic Wnt-Secreting Organizers

Current human pluripotent stem cell-derived kidney organoids contain nephron-like structures that lack organotypic patterning. It is thought that during human development, nephrons form their proximal-distal axial polarity in response to collecting duct-derived signals that are absent in kidney organoids. To delineate how nephron polarities establish, we profiled human kidney development by spatial transcriptomic approaches. Our analyses describe a new axial polarity in the nephron and demonstrate that the nephron proximal-distal polarity develops adjacent to a transcriptional boundary in the collecting duct where non-canonical WNT11 is downregulated and canonical WNT9B ligand is upregulated. The nephron region closest to this boundary in turn activates a series of canonical WNT target genes inferring positional nephron identities. To establish whether a canonical WNT source can improve organoid patterning to an in vivo-like state, we bioengineered self-organizing WNT-secreting synthetic organizers. Organizer-coupled kidney organoids respond to WNT ligands by forming expression gradients and developing distal cell identities. Tuning the WNT dose produced nephrons with continuous patterning along the proximal-distal axis. Strikingly, polarized iPSC-derived nephrons directed their distal tubules towards the WNT-source, indicating axial patterning and morphogenetic programs are tuned by WNTs from the synthetic organizers. Our data present a strategy to control organ patterning, build an artificial kidney, and highlights the power of synthetic organizer systems for advancing organoid models.

synthetic biology↗

bioRxiv2024

A Portable and Scalable Genomic Analysis Pipeline for Streptococcus pneumoniae Surveillance: GPS Pipeline

Ever increasing global sequencing capacity provides an unprecedented opportunity in utilising genomic information captured from whole-genome sequencing to enhance pathogen surveillance. However, there is a growing need for developing user-friendly tools to effectively analyse the increasing volume of data. To meet this need, we have developed a genomic analysis pipeline, GPS Pipeline, which is portable and scalable to analyse genomes of Streptococcus pneumoniae, a major bacterial pathogen that is estimated to cause 317,000 child deaths worldwide every year. The GPS Pipeline is based on Nextflow and containerisation technology, and designed to enable researchers generating public health relevant output, including in silico serotypes, pneumococcal lineages (i.e. GPSCs), multilocus sequence types, and antimicrobial susceptibilities against 20 commonly used antibiotics,with minimal software setup requirements and bioinformatic expertise, in order to analyse genomic data at scale with ease. The GPS Pipeline provides a streamlined workflow that improves responsiveness in genomic surveillance on pneumococci. Data SummaryThe GPS Pipeline is available on GitHub at github.com/GlobalPneumoSeq/gps-pipeline. Published data from the GPS Database is available on Monocle Data Viewer at data.monocle.sanger.ac.uk and associated sequence read files are searchable and downloadable in the European Nucleotide Archive at ebi.ac.uk/ena via their ERR accession numbers. Impact StatementThe GPS Pipeline advances global genomic surveillance of Streptococcus pneumoniae by providing a scalable, portable, and user-friendly tool for analysing whole-genome sequencing data. Leveraging Nextflow and containerisation technology, it minimises bioinformatics expertise requirements and infrastructure needs, making it particularly valuable in low- and middle-income countries where pneumococcal disease burden is high. This pipeline ensures reproducibility and stability across platforms, facilitating rapid and accurate pneumococci genomic analysis. By streamlining data processing, the GPS Pipeline enhances pathogen surveillance, generates evidence to support vaccine strategy development, and empowers researchers worldwide, ultimately contributing to improved public health outcomes.

genomics↗